James Starlight wrote:
Justin,
Could you tell me if I want to simulate self-organization of the pure
lipid bilayer starting from the initial random placed molecules in
water. Does this simulation need in pre-md NVT and NPT equilibration?
Some form of equilibration is always required.
What the average time for NPT? I think that If this stage should occur
it must be consist of long ( tens of NS ) preequilibration.
Temperature and pressure will likely converge within a few ns, but the
simulation is not equilibrated until the membrane has formed, I would say. This
is a process that can take hundreds of ns, or even us. Check the literature for
established protocols; there are reports of bilayer self-assembly already published.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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